EACR25-1034

Comprehensive screening of A-to-I editing in colorectal cancer: implications for tumour progression and therapeutic targeting.

M. Niemira¹, K. Chwialkowska², G. Sokolowska¹, A. Ostrowska¹, A. Zeller¹, W. Turska³, A. Michalska-Falkowska⁴, J. Reszec-Gielazyn⁵, M. Moniuszko⁶, A. Kretowski¹

¹Medical University of Bialystok, Clinical Research Centre, Bialystok, Poland
²Medical University of Bialystok, Centre for Bioinformatics and Data Analysis, Bialystok, Poland
³Medical University of Bialystok, Clinical Research Centre, [email protected], Poland
⁴Medical University of Bialystok, Biobank, Bialystok, Poland
⁵Medical University of Bialystok, Department of Medical Pathology, Bialystok, Poland
⁶Medical University of Bialystok, Centre of Regenerative Medicine, Bialystok, Poland

Introduction:

Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification that has been shown to influence gene expression, RNA stability, and protein function. In colorectal cancer (CRC), A-to-I editing may contribute to tumor progression by modulating key cellular pathways involved in proliferation, apoptosis, and metastasis. Despite its potential importance, a comprehensive investigation into the role of A-to-I editing in CRC has not yet been fully explored. This study aims to characterise A-to-I RNA editing patterns in CRC and explore its implications for tumor progression.

Material and method:

To identify A-to-I editing events, we performed high-throughput small RNA-sequencing on 116 CRC tissue samples and matched 119 normal colorectal tissues. The mapped output file was subjected to identifying reads containing A-to-G changes representing A-to-I editing in mature miRNA using the miRge 3.0 package. The A-to-I editing level was defined as the ratio of the mapped reads with changed nucleotides relative to the total mapped reads for each miRNA. A-to-I editing events were further analysed based on the respective percentage and expression level at the RPM scale. To reveal the biological function of the edited miRNAs, we identified putative target genes using Ingenuity Pathway Analysis (IPA), mirDB and TargetScanHuman 8.0 and performed WikiPathways analysis to investigate cancer-related pathways.

Result and discussion:

We identified four unique A-to-I miRNA editing hotspots. Among them, miR-200b-3p (logFC=1.17; FDR-adjusted p-value=1.91×10-15) was overedited, but miR-411-5p (logFC=-1.18; FDR-adjusted p-value=1.71×10-31), miR-497-5p (logFC=-1.06; FDR-adjusted p-value=6.66×10-18) and miR-99a-5p (logFC=-0.48; FDR-adjusted p-value=1.68×10-06) were underedited in tumors relative to normal tissues. All editing events were located in the seed region at the position 1-8 mature miRNAs.The functional analysis of edited miRNA target genes revealed that dysregulated pathways were mainly associated with EMT (Epithelial-Mesenchymal Transition) (FDR-adjusted p-value=3.44×10-10), PI3K/AKT pathway (FDR-adjusted p-value=2.48×10-11), mTOR pathway ((FDR-adjusted p-value=8.50×10-09), and cell cycle control (FDR-adjusted p-value=4.21×10-10). By ranking the PPI network nodes using the cytoHubba plugin of Cytoscape software, we found that CCND1, IGF1R, AKT1, PTEN, CDK6, CDK4, CDKN2A, SNAI1, GRB2, PRAS40 scores ranked in the top 10 hub genes.

Conclusion:

The findings highlight the potentially crucial role of A-to-I editing in the pathogenesis of CRC. Dysregulated A-to-I editing of identified miRNAs could contribute to tumorigenic processes, including metastasis, by altering key regulatory pathways involved in cancer progression.